CHANGES IN HMP VERSION 2.0 CHANGES * Added parallel computing to rpart cross validation * The best rpart tree can now be the tree with the smallest error or plus/minus 1 standard error * Changed rpart to run quicker by handling factors and numeric differently * Data.filter now works with numtaxa and perTaxa as NULL by keeping all taxa * Removed deprecated arguments * Added vignette containing code to reproduce figures in the DM-Rpart paper BUG FIXES * Fixed labeling error in rpart * Added error checking for rpart trees with 1 node and no surrogates CHANGES IN HMP VERSION 1.6 CHANGES * Added penalty for GA * Changed rpart to use cross validation to find the best tree instead of permutations * Changed KL to use MOM instead of MLE BUG FIXES * Fixed getBC so that it drops duplicates instead of crashing * Fixed estPi to handle groups with 1 sample CHANGES IN HMP VERSION 1.5.1 CHANGES * Added ability to use custom covar distance matrix * Added two new plotting functions * Added text to indicate logging with the pi plot function BUG FIXES * Fixed labels in GA plots and results * Fixed bug in Xmcupo.sevsample pvalue calculations * Fixed bug with plot.pi not passing plot title CHANGES IN HMP VERSION 1.5 CHANGES * Tidied up every function's code, comments, and variable names * Several function parameter names were changed. The old names remain to support backwards compatibility. * kullbackLieber was renamed to Kullback.Leibler. kullbackLieber now just calls Kullback.Leibler. * Added Plot.MDS to plot data * Added Est.PI to estimate the pi vector and plot it with Plot.Pi * Changed data.filter to allow for percentage based filtering * Added a function for testing paired data (Test.Paired) * Added a function that uses rpart to find groups within the data (DM.Rpart and DM.Rpart.Perm) * Added a function that use GA to find taxa that separate 2 groups (DM.GA and DM.GA.Consensus) BUG FIXES * DM.MoM can now take a single subject * Added 1 to the numerator and denominators for permutation tests to prevent pvalues = 0 CHANGES IN HMP VERSION 1.4.3 BUG FIXES * Fixed a bug in the DM.MoM function CHANGES IN HMP VERSION 1.4 CHANGES * Changed several functions to improve performance * MC.Xdc.statistic and MC.Xoc.statistics now calculates n.groups themselves * Xmcupo.sevsample now calculates K itself * Added a function to format and combine multiple data sets with different taxa * Added a Kullback Leiber function CHANGES IN HMP VERSION 1.3.1 CHANGES * Changed the MC example files to use "DM.MoM" instead of "dirmult" for speed BUG FIXES * Fixed a bug in MC.Xmcupo.statistics that produced a incorrect result under type="ha" CHANGES IN HMP VERSION 1.3 CHANGES * Updated several of the MC functions to perform power calculations on unbalanced designs, however it should be noted that this caused the Nrs parameter to change from a vector to a list for several functions. * Removed the initscalar parameter from the sevsample functions and replaced it with the value of gamma from the DM.MoM function. * Change the names of some functions so they all follow the same formatting. This change mainly affected internal functions. * Changed the wording of the return value in the MC functions from "effect size" to "size of the test statistics" to correctly describe what is being returned. * Changed the Barchart.data function to take a full title rather than just a taxa level. * Changed Xdc.sevsample to select between 'mle' and 'mom' estimators. * Added several warnings/notes clarifying that the value of MC should be >1000 in the MC.functions * Added several warnings/notes clarifying the use of different number of reads in a sample * Added two new functions: Xmcupo.effectsize and pioest BUG FIXES * Fixed a bug in MC.Xdc.statistics where k was not set to the right value under "ha".